text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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|---|---|---|---|---|---|---|
"""update the requirement source source title
Revision ID: 6edfa48316d0
Revises: 94d773680c08
Create Date: 2025-08-11 09:54:14.903883
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '6edfa48316d0'
down_revision = '94d773680c08'
branch_labels = None
depends_on =... | bcgov/EPIC.compliance | compliance-api/migrations/versions/6edfa48316d0_update_the_requirement_source_source_.py | .py | a543247838f4ced8 | 7.24 | 2 |
"""case file tables
Revision ID: 774870c99c95
Revises: f9a414e34ea4
Create Date: 2024-08-15 15:54:35.140278
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '774870c99c95'
down_revision = 'f9a414e34ea4'
branch_labels = None
depends_on = None
def upgrade():
... | bcgov/EPIC.compliance | compliance-api/migrations/versions/774870c99c95_case_file_tables.py | .py | bf0fc05df015ff85 | 7.24 | 2 |
# Copyright Spack Project Developers. See COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.generic import Package
from spack.package import *
import glob
class DunePardata(Package):
"""FIXME: Put a proper description of your package here."""
... | DUNE/dune_spack | spack_repo/dune_spack/packages/dune_pardata/package.py | .py | 8a28310a04bba682 | 7 | 0 |
# This package.py written by Liam O'Sullivan <liam.osullivan@uni-mainz.de>
# For reasons™, explicitly including root and geant4 as dependencies
# causes the build to fail (missing blas or whatevs).
# If you spack load root and geant4 it builds fine though.
from spack_repo.builtin.build_systems.cmake import CMakePackag... | DUNE/dune_spack | spack_repo/dune_spack/packages/dune_tms/package.py | .py | b8c085daa4c09488 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Duneanaobj(CM... | DUNE/dune_spack | spack_repo/dune_spack/packages/duneanaobj/package.py | .py | 9d9b76ca70ba0486 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Dunecalib(CMakePackage... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunecalib/package.py | .py | 0901a26de11100bd | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.generic import Package
from spack.package import *
class Dunedaqdataformats(Packa... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunedaqdataformats/package.py | .py | 9ac74691d3e7ee64 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Dunedataprep(CMakePack... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunedataprep/package.py | .py | a0314a3687ed4f31 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.generic import Package
from spack.package import *
class Dunedetdataformats(Packag... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunedetdataformats/package.py | .py | 0e93667096fec0f4 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Duneexamples(CMakePack... | DUNE/dune_spack | spack_repo/dune_spack/packages/duneexamples/package.py | .py | c5d86d9ccb0fe975 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Dunepdlegacy(CMakePack... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunepdlegacy/package.py | .py | 052f0549c99f0b7d | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Duneprototypes(CMakePa... | DUNE/dune_spack | spack_repo/dune_spack/packages/duneprototypes/package.py | .py | 60813f837f2baac3 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Dunesim(CMakePackage):... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunesim/package.py | .py | 18cc7500d9caa6a8 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
DUNE_PARDATA_DIR = "/cvmfs/d... | DUNE/dune_spack | spack_repo/dune_spack/packages/dunesw/package.py | .py | 8a465c658d17da68 | 7 | 0 |
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Duneutil(CMakePackage)... | DUNE/dune_spack | spack_repo/dune_spack/packages/duneutil/package.py | .py | 89bcdd1bbe9640ce | 7 | 0 |
# This package.py written by Liam O'Sullivan <liam.osullivan@uni-mainz.de>
# For reasons™, explicitly including root and geant4 as dependencies
# causes the build to fail (missing blas or whatevs).
# If you spack load root and geant4 it builds fine though.
from spack_repo.builtin.build_systems.cmake import CMakePackag... | DUNE/dune_spack | spack_repo/dune_spack/packages/edep_sim/package.py | .py | d5dab59184bd9fe0 | 7 | 0 |
"""API client for Phoenix-Bad Ottobrunn."""
from __future__ import annotations
import asyncio
import logging
import re
import aiohttp
from bs4 import BeautifulSoup
_LOGGER = logging.getLogger(__name__)
# API endpoints
POOL_URL = (
"https://phoenixbad.de/wp-admin/admin-ajax.php?action=updateLiveVisitors&area=Ba... | FaserF/ha-phoenixbad | custom_components/phoenix_bad/api.py | .py | f1fe8dcb8ac45c5a | 7 | 0 |
"""Config flow for Phönix-Bad Ottobrunn."""
from __future__ import annotations
import homeassistant.helpers.config_validation as cv
from homeassistant import config_entries
from .const import DOMAIN
CONFIG_SCHEMA = cv.config_entry_only_config_schema(DOMAIN)
class PhoenixBadConfigFlow(config_entries.ConfigFlow, do... | FaserF/ha-phoenixbad | custom_components/phoenix_bad/config_flow.py | .py | f1362fb3b8d4d664 | 7 | 0 |
"""DataUpdateCoordinator for Phoenix-Bad."""
from __future__ import annotations
import logging
from datetime import timedelta
import aiohttp
from homeassistant.core import HomeAssistant
from homeassistant.helpers.update_coordinator import DataUpdateCoordinator, UpdateFailed
from .api import OccupancyData, PhoenixBa... | FaserF/ha-phoenixbad | custom_components/phoenix_bad/coordinator.py | .py | 52afd5f7a5f90f42 | 7 | 0 |
"""Sensor platform for Phoenix-Bad Ottobrunn."""
import logging
from homeassistant.components.sensor import SensorEntity
from homeassistant.config_entries import ConfigEntry
from homeassistant.core import HomeAssistant
from homeassistant.helpers.entity_platform import AddEntitiesCallback
from homeassistant.helpers.up... | FaserF/ha-phoenixbad | custom_components/phoenix_bad/sensor.py | .py | fcf3c4be6f12b4cd | 7 | 0 |
"""Tests for Phoenix-Bad API client."""
import pytest
from custom_components.phoenix_bad.api import PhoenixBadApiClient, PhoenixBadParseError
def test_parse_response_success():
"""Test successful parsing of HTML response."""
html = '<div class="outer_wrapper" data-free="10"><div class="inner_wrapper" style=... | FaserF/ha-phoenixbad | tests/test_api.py | .py | bb22694551f2ac95 | 7.5 | 0 |
"""Test that all translation keys are present in EN and DE."""
import json
from pathlib import Path
import pytest
INTEGRATION_DIR = next(
p
for p in (Path(__file__).resolve().parent.parent / "custom_components").iterdir()
if p.is_dir() and p.name != "__pycache__"
)
STRINGS_FILE = INTEGRATION_DIR / "strin... | FaserF/ha-phoenixbad | tests/test_translations.py | .py | 653f2cc5228e0493 | 7.5 | 0 |
"""
This file serves as compatibility layer between this
limnd2 library maintained by Laboratory Imaging s.r.o. (https://github.com/Laboratory-Imaging/limnd2) and
nd2 library maintained by Talley Lambert (https://github.com/tlambert03/nd2)
It copies the interface of nd2 library, but uses limnd2 library on the "backend"... | Laboratory-Imaging/limnd2 | src/limnd2/nd2_compatability/nd2file_types.py | .py | c4f783a1e16ea844 | 7.3 | 3 |
from __future__ import annotations
from abc import ABC, abstractmethod
import copy
import json
from pathlib import Path
from copy import deepcopy
from dataclasses import is_dataclass, asdict
import re
import warnings
import numpy as np
import sys
from limnd2.attributes import ImageAttributes
from typing import TYPE_... | Laboratory-Imaging/limnd2 | src/limnd2/tools/conversion/LimImageSource.py | .py | 9cc2ffbf0b9e203f | 7.3 | 3 |
"""Reusable checkpoint storage for expensive experimental evidence jobs.
Timestamped ``evidence_jobs`` directories are immutable execution records. This
module provides a separate, stable cache for expensive numerical payloads that
can be validated and reused by later attempts. The cache key describes the
scientific... | tanlin2013/qlinks | experimental/jobs/evidence_cache.py | .py | 3155790c478fbcdc | 7.15 | 1 |
from __future__ import annotations
from dataclasses import dataclass
from itertools import product
from typing import Iterable
import numpy as np
import numpy.typing as npt
from qlinks.variables import ConfigEncoder, VariableLayout
def full_basis_from_layout(
layout: VariableLayout,
*,
sort: bool = Tru... | tanlin2013/qlinks | qlinks/basis/basis.py | .py | 0573be331465ca1e | 7.15 | 1 |
from __future__ import annotations
from typing import Any
import numpy as np
from numpy._typing import NDArray
def basis_configs_from_basis(basis: Any) -> NDArray[np.integer]:
"""Return explicit basis configurations for ArrayBasis or BinaryEncodedBasis.
Sparse/array builders usually expose this as ``basis.... | tanlin2013/qlinks | qlinks/basis/configs.py | .py | ddcb2d133d5bb414 | 7.15 | 1 |
from __future__ import annotations
from dataclasses import dataclass
from typing import Protocol, Sequence
from qlinks.basis.basis import Basis
from qlinks.constraints import Constraint, ConstraintCollection, SectorCondition
from qlinks.variables import VariableLayout
class BasisSolver(Protocol):
"""Protocol im... | tanlin2013/qlinks | qlinks/basis/solvers/base.py | .py | 7c4e42cff4ab8f79 | 7.15 | 1 |
from __future__ import annotations
from dataclasses import dataclass
from itertools import product
from typing import Sequence
import numpy as np
from qlinks.basis.basis import Basis
from qlinks.constraints import Constraint, SectorCondition, all_satisfied
from qlinks.variables import VariableLayout
@dataclass(fro... | tanlin2013/qlinks | qlinks/basis/solvers/brute_force.py | .py | 0aff82ee03bbb382 | 7.15 | 1 |
class CustomStep:
"""This class helps you perform operations on a SAS Studio Custom Step programmatically"""
def __init__(self, custom_step_file:str = None, name: str =None,
creationTimeStamp=None, modifiedTimeStamp=None, createdBy: str=None,
modifiedBy: str =None, displayName... | SundareshSankaran/py-sas-studio-custom-steps | src/py_sas_studio_custom_steps/custom_step.py | .py | cc0cd99fc35230e0 | 7.15 | 1 |
#!/usr/bin/env python3
"""Verification hook — runs after every Edit/Write/MultiEdit and feeds failures back.
Adopted from agent-ready-projects v1.14.0 ("Verification Hooks"). The point is who
carries the error message: without this, the agent edits, stops, and waits for a human
to run the tests and paste the failure b... | ducroq/energydatahub | .claude/hooks/verify_edit.py | .py | 1de87c36d51968ba | 7 | 0 |
"""
EnergyZero API Collector
-------------------------
Collects energy prices from EnergyZero API using the new base collector
architecture.
File: collectors/energyzero.py
Created: 2025-10-25
Author: Energy Data Hub Project
Description:
Implements BaseCollector for EnergyZero data. Handles real-time and
day-a... | ducroq/energydatahub | collectors/energyzero.py | .py | a502d1a343afd9c8 | 7 | 0 |
"""
ENTSOG Gas Flows Collector
--------------------------
Fetches European gas flow data from the ENTSOG Transparency Platform.
File: collectors/entsog_flows.py
Created: 2025-01-19
Description:
Collects gas flow data from ENTSOG (European Network of Transmission
System Operators for Gas) Transparency Platform... | ducroq/energydatahub | collectors/entsog_flows.py | .py | 0876e8513b88ecc1 | 7 | 0 |
"""
EPEX SPOT Market Collector
----------------------------
Collects day-ahead energy prices from EPEX SPOT market via Awattar API using
the new base collector architecture.
File: collectors/epex.py
Created: 2025-10-25
Author: Energy Data Hub Project
Description:
Implements BaseCollector for EPEX SPOT data. Handl... | ducroq/energydatahub | collectors/epex.py | .py | 1a7f15b0df0d8893 | 7 | 0 |
"""
Backfill missing ENTSO-E price data into existing energy_price_forecast files.
Scans all timestamped price files, identifies those missing 'entsoe' (NL) and/or
'entsoe_de' (DE) datasets, fetches historical prices from the ENTSO-E API,
and merges them back into the encrypted files.
Usage:
python scripts/backfi... | ducroq/energydatahub | scripts/backfill_entsoe.py | .py | 8e1d8db4008a2e4f | 7 | 0 |
"""
Backfill broken gas storage timestamps in historical data files.
A bug in pd.concat(ignore_index=True) caused GIE storage data to lose its
gasDayStart index, resulting in integer keys ('0', '1', '2') instead of ISO
timestamps. The data values are intact; only the keys need reconstruction
using metadata start_time ... | ducroq/energydatahub | scripts/backfill_gas_storage.py | .py | 4fe4033ac8484352 | 7 | 0 |
"""
Command-line interface for CartoSym Transcoder.
"""
import argparse
import json
import sys
from pathlib import Path
from typing import Optional
from antlr4 import CommonTokenStream, FileStream
from jsonschema import ValidationError
from jsonschema import validate as jsonschema_validate
from cartosym_transcoder.g... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/cli.py | .py | 0c60b81b54132d79 | 7.15 | 1 |
"""
Abstract base class for format codecs.
Each codec provides a reader (format → Style) and a writer (Style → format).
"""
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Any, List, Union
from ..models.styles import Style
class CodecReader(ABC):
"""Abstract reader: converts a s... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/base.py | .py | ca2768f18a0dbd1e | 7.15 | 1 |
"""
CSCSS reader — parse CartoSym-CSS files into Style models.
Delegates to the existing :class:`~cartosym_transcoder.parser.CartoSymParser`.
"""
from pathlib import Path
from typing import Union
from ...models.styles import Style
from ...parser import CartoSymParser
from ..base import CodecReader
class CscssReade... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/cscss/reader.py | .py | b7b08072b263ff77 | 7.15 | 1 |
"""
CSCSS writer — serialise Style models to CartoSym-CSS text.
Delegates to :meth:`~cartosym_transcoder.converter.Converter.style_to_cscss`.
"""
from ...converter import Converter
from ...models.styles import Style
from ..base import CodecWriter
class CscssWriter(CodecWriter):
"""Write a Style model as ``.cscs... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/cscss/writer.py | .py | 9520d84c4111b788 | 7.15 | 1 |
"""
CS-JSON reader — parse CartoSym-JSON files into Style models.
Delegates to :meth:`~cartosym_transcoder.converter.Converter.csjson_to_style`.
"""
from pathlib import Path
from typing import Union
from ...converter import Converter
from ...models.styles import Style
from ..base import CodecReader
class CsjsonRea... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/csjson/reader.py | .py | 644a905ecfa068fe | 7.15 | 1 |
"""
CS-JSON writer — serialise Style models to CartoSym-JSON.
Delegates to :meth:`~cartosym_transcoder.converter.Converter.cscss_to_csjson`
(which accepts a Style model directly and produces a validated dict).
"""
import json
from typing import Any, Union
from ...converter import Converter
from ...models.styles impo... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/csjson/writer.py | .py | b5521a82b48eff8f | 7.15 | 1 |
"""
MapLibre / MapBox GL Style reader — parse MapLibre style JSON into Style models.
.. note::
This is a **stub**. Implementation is tracked in ROADMAP §3.4.
"""
from pathlib import Path
from typing import Union
from ...models.styles import Style
from ..base import CodecReader
class MaplibreReader(CodecReader):... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/maplibre/reader.py | .py | 0e4b6543745826a7 | 7.15 | 1 |
"""
MapLibre / MapBox GL Style writer — serialise Style models to MapLibre
style JSON.
.. note::
This is a **stub**. Implementation is tracked in ROADMAP §3.4.
"""
from ...models.styles import Style
from ..base import CodecWriter
class MaplibreWriter(CodecWriter):
"""Write a Style model as MapLibre / MapBox ... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/maplibre/writer.py | .py | 6593954ad2932dcd | 7.15 | 1 |
"""
Scalar formatting conventions for the SLD/SE codec.
SLD/SE ``se:SvgParameter`` values and XML attributes are bare numeric/hex
strings — unlike CartoSym's ``{unit: value}`` dict convention for
:class:`~cartosym_transcoder.models.types.UnitValue`, SE 1.1.0 core has no
unit-of-measure attribute on these parameters, s... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/sld_se/_types.py | .py | f6d3ea62b0481e8c | 7.15 | 1 |
"""
XML namespace constants and small ``lxml`` element-building helpers shared
by :mod:`_filter`, :mod:`_symbolizer`, :mod:`reader`, and :mod:`writer`.
"""
from typing import Optional
from lxml import etree
SLD_NS = "http://www.opengis.net/sld"
SE_NS = "http://www.opengis.net/se"
OGC_NS = "http://www.opengis.net/ogc... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/sld_se/_xml_helpers.py | .py | 3180346f2fd9fa08 | 7.15 | 1 |
"""
SLD/SE reader — parse OGC Styled Layer Descriptor / Symbology Encoding XML
into Style models.
Scope: vector symbolizers plus basic Part-1 raster/coverage styling. See
``writer.py``'s module docstring and ``docs/sld_se_mapping_issues.md`` for
the exact scope boundary. Out-of-scope SLD/SE constructs (e.g. advanced
r... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/codecs/sld_se/reader.py | .py | 845a70400d15b17e | 7.15 | 1 |
"""
CQL2-JSON serialisation — conversion between expression models and CQL2-JSON dicts.
The CQL2-JSON serialisation is currently handled by:
* **Serialisation** (model → JSON dict): methods on the expression model classes
(``to_cql2_json()``) and the ``ast_converter._convert_expression_to_json_selector()``.
* **Des... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/expressions/cql2_json.py | .py | 591c21d4b10758a0 | 7.15 | 1 |
"""
CQL2-Text serialisation — write-back of expressions to CQL2-Text syntax.
The CQL2-Text write-back logic is currently implemented inline in
:meth:`~cartosym_transcoder.converter.Converter._format_selector_expr`.
This module provides a public entry-point that delegates to that method.
"""
from typing import Any
fr... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/expressions/cql2_text.py | .py | a88b2769a28276bc | 7.15 | 1 |
"""
Base Pydantic models and utilities for CartoSym.
"""
from abc import ABC
from typing import Any, Dict, List, Optional, Union
from pydantic import BaseModel, ConfigDict, Field
class BaseCartoSymModel(BaseModel):
"""
Base class for all CartoSym models.
Provides common configuration and utilities for ... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/models/base.py | .py | 38d1308dbcf7ab65 | 7.15 | 1 |
"""
Core style and rule models for CartoSym.
Based on the JSON Schema definitions for style, stylingRule, and metadata.
"""
from typing import Any, Dict, List, Optional, Union
from pydantic import Field, field_validator, model_validator
from .base import BaseCartoSymModel, CommentMixin
# Import symbolizers
from .s... | maxcollombin/CartoSymTranscoder | src/cartosym_transcoder/models/styles.py | .py | 7437477a237148f6 | 7.15 | 1 |
from pathlib import Path
from typing import Any
from mlrepromutate.engine.runner import ExecutionResult, ExperimentRunner
from mlrepromutate.engine.sandbox import ProjectSandbox
from mlrepromutate.models import (
MutationCandidate,
MutationOutcome,
MutationResult,
)
from mlrepromutate.operators.base import... | ilyuka/MLReproMutate | src/mlrepromutate/engine/evaluator.py | .py | 001782881f4dd9c0 | 7 | 0 |
from dataclasses import dataclass, field
from enum import StrEnum
from pathlib import Path
from typing import Any
class MutationOutcome(StrEnum):
"""Possible outcomes of evaluating a mutation."""
KILLED = "killed"
SURVIVED = "survived"
INVALID = "invalid"
EQUIVALENT = "equivalent"
TIMEOUT = "... | ilyuka/MLReproMutate | src/mlrepromutate/models.py | .py | c81999ca8bcf5928 | 7 | 0 |
from abc import ABC, abstractmethod
from collections.abc import Iterable
from pathlib import Path
from mlrepromutate.models import MutationCandidate
class MutationOperator(ABC):
"""Base interface for reproducibility mutation operators."""
@property
@abstractmethod
def name(self) -> str:
"""R... | ilyuka/MLReproMutate | src/mlrepromutate/operators/base.py | .py | 396bc21f93052289 | 7 | 0 |
import googlemaps
from googlemaps.exceptions import ApiError, TransportError
from config import GEOCODING_API_KEY
class SearchLocal:
def __init__(self, latitude: float, longitude: float):
self.gmaps = googlemaps.Client(key=GEOCODING_API_KEY)
self.latitude = latitude
self.longitude = longit... | DoctorSolo/Geocode-Aplication-Google-Cloud | src/SearchLocal.py | .py | bc8ded484b6fd7cc | 7.15 | 1 |
"""Demonstration of Advanced Acquisition Strategies.
This script demonstrates that Phase 2 acquisition functions work as intended:
- BALD: Selects samples with high mutual information
- Core-Set: Selects diverse samples covering the embedding space
- BatchBALD/DPP: Selects diverse batches avoiding redundancy
- EGL: Se... | HFooladi/molax | examples/acquisition_strategies_demo.py | .py | 5eb473c0ec329af6 | 7.15 | 1 |
"""Active Learning Benchmark - Efficient jraph implementation.
Compares acquisition strategies:
- Random sampling (baseline)
- Uncertainty sampling (MC dropout variance)
- Combined uncertainty + Core-Set diversity
Key optimization: Batch all data once, use masking for active learning.
This avoids JIT recompilation an... | HFooladi/molax | examples/active_learning_benchmark.py | .py | 0484aa4f3f5c93fd | 7.15 | 1 |
"""Calibration Comparison: MC Dropout vs Ensemble vs Evidential.
This example demonstrates the calibration metrics module by:
1. Training three model types on ESOL dataset
2. Computing calibration metrics for each
3. Visualizing reliability diagrams
4. Applying temperature scaling for post-hoc calibration
The example... | HFooladi/molax | examples/calibration_comparison.py | .py | d87127370c70197d | 7.15 | 1 |
"""Efficient active learning with jraph - fixed batch approach.
Key insight: Batch ALL training data once, use index masking for active learning.
This avoids JIT recompilation from changing shapes.
Protocol note: the model is re-initialized at the start of every acquisition
round. Warm-starting one model across round... | HFooladi/molax | examples/simple_active_learning.py | .py | 3f0d20548fa6679b | 7.15 | 1 |
"""Batch-aware acquisition functions for active learning.
These methods consider interactions between samples in a batch to select
diverse, informative batches rather than independently selecting top samples.
Includes:
- BatchBALD: Greedy selection maximizing joint mutual information
- DPP: Determinantal Point Proces... | HFooladi/molax | molax/acquisition/batch_aware.py | .py | ab70aaa061e494f3 | 7.15 | 1 |
"""Core-Set selection for active learning.
Core-Set selection uses k-center greedy algorithm in the model's embedding
space to select a diverse and representative subset of samples. This approach
aims to minimize the maximum distance from any point to its nearest selected
point, providing good coverage of the data dis... | HFooladi/molax | molax/acquisition/coreset.py | .py | 0394f12a08e3263e | 7.15 | 1 |
"""Expected Model Change acquisition functions.
Expected Gradient Length (EGL) selects samples that would cause the largest
change in model parameters if labeled. This is approximated by computing the
gradient of the loss with respect to model parameters for each sample, using
the model's prediction as a pseudo-label.... | HFooladi/molax | molax/acquisition/expected_change.py | .py | 8651a361f84edc7d | 7.15 | 1 |
"""Deep Ensemble models for improved uncertainty quantification.
Deep Ensembles train N independent models with different random initializations.
Uncertainty is estimated via prediction disagreement (epistemic) plus
average predicted variance (aleatoric).
Reference: Lakshminarayanan et al., "Simple and Scalable Predi... | HFooladi/molax | molax/models/ensemble.py | .py | b4aafc6de21abaaf | 7.15 | 1 |
"""Graph Attention Networks using jraph for efficient batched processing.
GAT uses learned attention weights to dynamically weight neighbor contributions,
enabling adaptive aggregation based on node relevance.
"""
from dataclasses import dataclass
from typing import Sequence, Tuple
import flax.nnx as nnx
import jax.... | HFooladi/molax | molax/models/gat.py | .py | 159d6a4ca930059e | 7.15 | 1 |
"""Message Passing Neural Networks using jraph for efficient batched processing.
MPNN extends GCN by incorporating edge features in the message computation,
enabling the model to leverage bond information for molecular property prediction.
"""
from dataclasses import dataclass
from typing import Literal, Sequence, Tu... | HFooladi/molax | molax/models/mpnn.py | .py | c35fde4feacfb8a3 | 7.15 | 1 |
"""Data utilities for molecular graph datasets using jraph for efficient batching."""
from pathlib import Path
from typing import List, Optional, Tuple, Union
import jax.numpy as jnp
import jraph
import numpy as np
import pandas as pd
from rdkit import Chem
from .featurizers import DEFAULT_FEATURIZER, get_atom_featu... | HFooladi/molax | molax/utils/data.py | .py | 0606ccd881d26682 | 7.15 | 1 |
"""Atom featurizers for converting RDKit atoms to node feature vectors.
Two featurizers are registered:
- ``"basic"`` (default): six raw descriptor values. Kept as the default so that
existing code and saved configurations keep working unchanged.
- ``"rich"``: 29-dimensional one-hot encoding. Raw descriptors span v... | HFooladi/molax | molax/utils/featurizers.py | .py | 16d535cb573f6b0a | 7.15 | 1 |
import datetime
import logging
import sys
from pathlib import Path
from typing import Optional
def setup_logger(
name: str = "molax",
log_level: int = logging.INFO,
log_file: Optional[str] = None,
console_output: bool = True,
) -> logging.Logger:
"""Set up a logger with both file and console handl... | HFooladi/molax | molax/utils/logger.py | .py | 73ea275b8c740496 | 7.15 | 1 |
"""Tests for acquisition functions using jraph graphs."""
import jax.numpy as jnp
import pytest
from molax.acquisition import (
combined_acquisition,
diversity_sampling,
uncertainty_sampling,
)
from molax.models.gcn import GCNConfig, UncertaintyGCN
from molax.utils.data import smiles_to_jraph
@pytest.fi... | HFooladi/molax | tests/test_acquisition.py | .py | a453699ff007e611 | 7.65 | 1 |
"""Tests for BALD acquisition functions."""
import flax.nnx as nnx
import jax.numpy as jnp
import pytest
from molax.acquisition.bald import (
bald_sampling,
ensemble_bald_sampling,
evidential_bald_sampling,
)
from molax.models.ensemble import DeepEnsemble, EnsembleConfig
from molax.models.evidential impor... | HFooladi/molax | tests/test_bald.py | .py | 71f5d41c60236c61 | 7.65 | 1 |
"""Tests for calibration metrics and visualization."""
import jax.numpy as jnp
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pytest
from molax.metrics import (
TemperatureScaling,
calibration_error_per_sample,
compute_calibration_curve,
create_calibration_report,
eval... | HFooladi/molax | tests/test_calibration.py | .py | b78c650098721a5e | 7.65 | 1 |
"""Tests for Core-Set acquisition functions."""
import flax.nnx as nnx
import jax
import jax.numpy as jnp
import pytest
from molax.acquisition.coreset import (
coreset_from_embeddings,
coreset_sampling,
coreset_sampling_with_scores,
)
from molax.models.ensemble import DeepEnsemble, EnsembleConfig
from mol... | HFooladi/molax | tests/test_coreset.py | .py | b719e3018fa9f71a | 7.65 | 1 |
"""Tests for Deep Ensemble models."""
import flax.nnx as nnx
import jax.numpy as jnp
import jraph
import pytest
from molax.models.ensemble import (
DeepEnsemble,
EnsembleConfig,
create_ensemble_optimizers,
eval_ensemble_step,
get_ensemble_uncertainties,
train_ensemble_step,
)
from molax.models... | HFooladi/molax | tests/test_ensemble.py | .py | 519e14246b8fa2d1 | 7.65 | 1 |
"""Tests for Evidential Deep Learning models."""
import flax.nnx as nnx
import jax.numpy as jnp
import jraph
import pytest
from molax.models.evidential import (
EvidentialConfig,
EvidentialGCN,
EvidentialHead,
create_evidential_optimizer,
eval_evidential_step,
evidential_loss,
get_evidenti... | HFooladi/molax | tests/test_evidential.py | .py | 8917a4c3d8946f70 | 7.65 | 1 |
"""Tests for Expected Gradient Length acquisition functions."""
import flax.nnx as nnx
import jax.numpy as jnp
import pytest
from molax.acquisition.expected_change import (
egl_acquisition,
egl_sampling,
egl_sampling_batched,
)
from molax.models.gcn import GCNConfig, UncertaintyGCN
from molax.utils.data i... | HFooladi/molax | tests/test_expected_change.py | .py | 170b63899ea8fc5a | 7.65 | 1 |
"""Tests for atom featurizers and their integration with smiles_to_jraph."""
import jax.numpy as jnp
import pytest
from rdkit import Chem
from molax.utils.data import MolecularDataset, batch_graphs, smiles_to_jraph
from molax.utils.featurizers import (
ATOM_FEATURIZERS,
DEFAULT_FEATURIZER,
get_atom_featur... | HFooladi/molax | tests/test_featurizers.py | .py | 412fed044255022e | 7.65 | 1 |
"""Guardrails against Flax NNX API drift.
molax targets the Flax NNX API as of flax>=0.12 (verified against flax 0.12.2 /
jax 0.9.0 / optax 0.2.6). The patterns asserted here are the ones that have
already changed once in NNX's history and would otherwise break silently in an
example script rather than loudly in CI.
"... | HFooladi/molax | tests/test_flax_compat.py | .py | 206f3c305faea758 | 7.65 | 1 |
"""Make Resource.resource_definition_accession_id nullable.
Revision ID: 3a1fe0851e06
Revises:
Create Date: 2025-11-10 18:42:40.749914
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "3a1fe0851e06"
down_revision: str ... | maraxen/praxis | .agent/backups/alembic_20260121/versions/3a1fe0851e06_make_resourceorm_resource_definition_.py | .py | 271983bcf1dbbda6 | 7.35 | 4 |
"""Remove unique constraint from name in PLR definitions.
Revision ID: 577d92edf9a5
Revises: 3a1fe0851e06
Create Date: 2025-12-21 12:48:00.000000
"""
from collections.abc import Sequence
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "577d92edf9a5"
down_revision: str | Sequence[str]... | maraxen/praxis | .agent/backups/alembic_20260121/versions/577d92edf9a5_remove_unique_from_name.py | .py | b2c80e157f6c6c93 | 7.35 | 4 |
"""add properties_json to resource_definition.
Revision ID: a7f3e8c9d2b1
Revises: cd193888759e
Create Date: 2025-12-22
"""
from collections.abc import Sequence
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "a7f3e8c... | maraxen/praxis | .agent/backups/alembic_20260121/versions/a7f3e8c9d2b1_add_properties_json_to_resource_definition.py | .py | 0e5181e3223d621c | 7.35 | 4 |
"""add deck_layout_path to function_protocol_definitions.
Revision ID: b8c4d5e6f7a2
Revises: a7f3e8c9d2b1
Create Date: 2026-01-02
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "b8c4d5e6f7a2"
down_revision: str | None... | maraxen/praxis | .agent/backups/alembic_20260121/versions/b8c4d5e6f7a2_add_deck_layout_path_to_protocol_defs.py | .py | be1ee16e60c1f7b2 | 7.35 | 4 |
"""add_maintenance_and_location_columns
Revision ID: bb6b6f27cedb
Revises: d1e2f3a4b5c6
Create Date: 2026-01-02 10:54:27.953651
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = 'bb6b6f27cedb'
down_revision: Union[str, Seq... | maraxen/praxis | .agent/backups/alembic_20260121/versions/bb6b6f27cedb_add_maintenance_and_location_columns.py | .py | 198b8e06aa306db5 | 7.35 | 4 |
"""add data_views_json to function_protocol_definitions.
Revision ID: c9d5e6f7a8b3
Revises: b8c4d5e6f7a2
Create Date: 2026-01-02
"""
from collections.abc import Sequence
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
from alembic import op
# revision identifiers, used by Alembic.
revision: str ... | maraxen/praxis | .agent/backups/alembic_20260121/versions/c9d5e6f7a8b3_add_data_views_json_to_protocol_defs.py | .py | a7b883a1239202fa | 7.35 | 4 |
"""add_dynamic_filter_columns_to_resource_definitions.
Revision ID: cd193888759e
Revises: 577d92edf9a5
Create Date: 2025-12-21 19:33:48.579424
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "cd193888759e"
down_revisio... | maraxen/praxis | .agent/backups/alembic_20260121/versions/cd193888759e_add_dynamic_filter_columns_to_resource_.py | .py | 1da55846045819d1 | 7.35 | 4 |
"""add computation_graph_json, source_hash, graph_cached_at to function_protocol_definitions.
Revision ID: e2f3a4b5c6d7
Revises: bb6b6f27cedb
Create Date: 2026-01-03
"""
from collections.abc import Sequence
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
from alembic import op
# revision identif... | maraxen/praxis | .agent/backups/alembic_20260121/versions/e2f3a4b5c6d7_add_computation_graph_to_protocol_defs.py | .py | e7ac96b9626945ca | 7.35 | 4 |
"""add bytecode cache columns to function_protocol_definitions.
Revision ID: g4b5c6d7e8f9
Revises: f3a4b5c6d7e8
Create Date: 2026-01-05
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "g4b5c6d7e8f9"
down_revision: str ... | maraxen/praxis | .agent/backups/alembic_20260121/versions/g4b5c6d7e8f9_add_bytecode_cache_to_protocol_defs.py | .py | 8cd69dd79041b91a | 7.35 | 4 |
"""add required_plr_category to protocol_asset_requirements.
Revision ID: h5c6d7e8f9a0
Revises: g4b5c6d7e8f9
Create Date: 2026-01-10
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "h5c6d7e8f9a0"
down_revision: str | N... | maraxen/praxis | .agent/backups/alembic_20260121/versions/h5c6d7e8f9a0_add_required_plr_category_to_assets.py | .py | 78042a8b671dd9d0 | 7.35 | 4 |
"""add is_reusable to resource_definitions.
Revision ID: i6d7e8f9g0h1
Revises: 3a1fe0851e06
Create Date: 2026-01-16
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision: str = "i6d7e8f9g0h1"
down_revision: str | None = "3a1fe0851e... | maraxen/praxis | .agent/backups/alembic_20260121/versions/i6d7e8f9g0h1_add_is_reusable_to_resource_definitions.py | .py | 7eac72b1149da04a | 7.35 | 4 |
#!/usr/bin/env python3
"""Submit pending Jules dispatches from the agent database."""
import sqlite3
import subprocess
import tempfile
import time
import os
DB_PATH = "/Users/mar/Projects/praxis/.agent/agent.db"
def get_pending_dispatches():
"""Get all pending Jules dispatches."""
conn = sqlite3.connect(DB_PA... | maraxen/praxis | .agent/scripts/submit_jules.py | .py | 61e05551960b1cad | 7.35 | 4 |
#!/usr/bin/env python3
"""
Architecture Diagram Generator
Automated tool for senior architect tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class ArchitectureDiagramGenerator:
"""Main class for architecture diagram generator functionali... | maraxen/praxis | .agent/skills/senior-architect/scripts/architecture_diagram_generator.py | .py | 16d48c6543db51c6 | 7.35 | 4 |
#!/usr/bin/env python3
"""
Dependency Analyzer
Automated tool for senior architect tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class DependencyAnalyzer:
"""Main class for dependency analyzer functionality"""
def __init__(self... | maraxen/praxis | .agent/skills/senior-architect/scripts/dependency_analyzer.py | .py | 7ca90d81bccb129c | 7.35 | 4 |
#!/usr/bin/env python3
"""
Project Architect
Automated tool for senior architect tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class ProjectArchitect:
"""Main class for project architect functionality"""
def __init__(self, targ... | maraxen/praxis | .agent/skills/senior-architect/scripts/project_architect.py | .py | 888c16bf91e5b419 | 7.35 | 4 |
#!/usr/bin/env python3
"""
Code Quality Analyzer
Automated tool for senior fullstack tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class CodeQualityAnalyzer:
"""Main class for code quality analyzer functionality"""
def __init__... | maraxen/praxis | .agent/skills/senior-fullstack/scripts/code_quality_analyzer.py | .py | 936eef2d89bebbd6 | 7.35 | 4 |
#!/usr/bin/env python3
"""
Fullstack Scaffolder
Automated tool for senior fullstack tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class FullstackScaffolder:
"""Main class for fullstack scaffolder functionality"""
def __init__(s... | maraxen/praxis | .agent/skills/senior-fullstack/scripts/fullstack_scaffolder.py | .py | 4312f549f0277246 | 7.35 | 4 |
#!/usr/bin/env python3
"""
Project Scaffolder
Automated tool for senior fullstack tasks
"""
import os
import sys
import json
import argparse
from pathlib import Path
from typing import Dict, List, Optional
class ProjectScaffolder:
"""Main class for project scaffolder functionality"""
def __init__(self, t... | maraxen/praxis | .agent/skills/senior-fullstack/scripts/project_scaffolder.py | .py | 9844377e81cd5953 | 7.35 | 4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
UI/UX Pro Max Core - BM25 search engine for UI/UX style guides
"""
import csv
import re
from pathlib import Path
from math import log
from collections import defaultdict
# ============ CONFIGURATION ============
DATA_DIR = Path(__file__).parent.parent / "data"
MAX_RE... | maraxen/praxis | .agent/skills/ui-ux-pro-max/scripts/core.py | .py | 8949bb622be5ea28 | 7.35 | 4 |
#!/usr/bin/env python3
"""
Start one or more servers, wait for them to be ready, run a command, then clean up.
Usage:
# Single server
python scripts/with_server.py --server "npm run dev" --port 5173 -- python automation.py
python scripts/with_server.py --server "npm start" --port 3000 -- python test.py
... | maraxen/praxis | .agent/skills/webapp-testing/scripts/with_server.py | .py | b0dcf4918935b795 | 7.85 | 4 |
import asyncio
import os
from logging.config import fileConfig
from sqlalchemy import pool
from sqlalchemy.engine import Connection
from sqlalchemy.ext.asyncio import async_engine_from_config
from sqlmodel import SQLModel
from alembic import context
from praxis.backend.utils.db import Base as PraxisBase
# --- MODIFIC... | maraxen/praxis | alembic/env.py | .py | 24c715d16a2838b3 | 7.35 | 4 |
"""N5-B categorization: Matches / Conflicts / Omissions for clarification
cards (W4, FR-7).
The derivation reads ONLY the Layer 2/3 output a clarify exit already carries
-- a ``GroundingExitPayload``'s candidates, slot and message -- plus nothing
else: no kernel reads, no model call, no new grounding lookups. It exist... | maraxen/praxis | coxswain/src/coxswain/categorize.py | .py | 209142dfdfe55780 | 7.35 | 4 |
#!/usr/bin/env python
import sys
sys.path.append("/app")
import click
import asyncio
from typing import get_type_hints
import openpyxl
from openpyxl.utils import get_column_letter
from tqdm import tqdm
from sqlmodel import delete, select
from sqlalchemy.orm import sessionmaker
from sqlalchemy.ext.asyncio import A... | colorado-cancer-center/ecco | backend/app/commands/import_cancer_disparities.py | .py | d8ee1ea5efb01b14 | 7.3 | 3 |
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